I think I've discovered a bit of welcome news with the recent iTunes 12.3.3 update:
Apple has either fixed a bug, or thrown a bone to users who use iTunes to sync new app updates to their devices -- when the option to "Sort by Date Added" is selected, the app list/picker now takes into the account the date the app was last updated, and puts those apps at the top of the list.
Prior to this, the list would actually be sorted by the date the app was added to an iTunes library, while listing the date of the purchase/update below the app name.
So now, it seems that iTunes is using the Purchase Date field, and not Date Added field, to do the sorting. Note that the former and latter are not always necessarily the same. The majority of my apps all carry the same Date Added from late last year, when I moved to a new SSD, and dragged my media library on top of a clean install of iTunes. Only the app purchases made since then reflect the same Date Added as Purchase Date, and the latter can be even later, if the app has been updated since then.
One example -- my IMDb app reflects a Date Added of 12/1/15 (new iTunes library on new drive), and since it was updated today, Purchase Date and Date Modified of 3/25/16. Prior to this, it would have been listed with the Purchase Date of 3/25/16 below the name, but the app itself wouldn't appear at the top of the list; it would be sorted by the 12/1/15 when it was added to the library, and thus end up far down the list.
Technically, that was correct, as the app was added to my library on 12/1/15, and did exactly as the option said. However, that did not take into account the possible discrepancies between that date purchased/updated and the date added. If a user does a mass migration like I did, it would throw the whole thing out of whack. The way it works now with 12.3.3 makes more sense to me, though they haven't corrected the name of the option to reflect that.
I thought I might have been seeing things, and missed this before, but I checked 12.3.2 on a backup volume with 10.11.3, and it did not do this.
Even though manual selection of app updates is still required, the difficultly is lessened by the fact that the latest updates appear at the top of the app listing, not buried somewhere further down.